scFlow - Cell-type and Cluster Overview Report
15 October, 2020
Dimensionality Reduction Plots
Cell-types
This two-dimensional embedding of cells should demonstrate spatial separation of major cell-types; if not, it may be useful to manually re-annotate cell-types with reference to cell-type associated marker genes, and/or revise dimensionality reduction and/or clustering parameters.
Figure: UMAP_Liger plot of cell-types. Each cell is coloured by annotated cell-type.
Top Cell-type Marker Genes Table
Top Cell-Type Marker Genes Plot
Figure: Top marker genes for cells grouped by cell-type. Point colour represents expression and size represents the fraction of cells within the group expressing the gene.
Clusters
Optimal clustering parameters should provide a level of granularity sufficient to identify minority cell-types as distinct numbered clusters. If any cluster encompasses an adjacent small, well-separated cluster, the clustering parameters should be revised to allow for the annotation of the potential minority cell-type.
Figure: UMAP_Liger plot of clusters. Each cell is coloured by annotated cluster.
Top Cluster Marker Genes Table
Top Cluster Marker Genes Plot
Figure: Top marker genes for cells grouped by cluster. Point colour represents expression and size represents the fraction of cells within the group expressing the gene.
Manifest
Figure: UMAP_Liger plot of cells by manifest.
Group
Figure: UMAP_Liger plot of cells by group.
Sex
Figure: UMAP_Liger plot of cells by sex.
Cell-type Proportion Plots
These plots illustrate the absolute cell numbers and relative proportions of cell-types in the overall experiment (“all”), and within the groups: manifest, group, sex. To examine statistically significant differences in cell-type proportions, see the Dirichlet model results and report(s).
All
Figure: Absolute cell-type numbers by all.
Figure: Relative cell-type numbers by all.
Manifest
Figure: Absolute cell-type numbers by manifest.
Figure: Relative cell-type numbers by manifest.
Group
Figure: Absolute cell-type numbers by group.
Figure: Relative cell-type numbers by group.
Sex
Figure: Absolute cell-type numbers by sex.
Figure: Relative cell-type numbers by sex.
Cell-type Metric Plots
These plots summarize the distribution of various cell metrics (pc_mito, pc_ribo, total_counts, total_features_by_counts) for each cell-type.
pc_mito
Figure: Average pc_mito by cell-type. Bars represent mean average +/- SEM.
Figure: Distributions of pc_mito by cell-type.
pc_ribo
Figure: Average pc_ribo by cell-type. Bars represent mean average +/- SEM.
Figure: Distributions of pc_ribo by cell-type.
total_counts
Figure: Average total_counts by cell-type. Bars represent mean average +/- SEM.
Figure: Distributions of total_counts by cell-type.
total_features_by_counts
Figure: Average total_features_by_counts by cell-type. Bars represent mean average +/- SEM.
Figure: Distributions of total_features_by_counts by cell-type.
scFlow v0.5.1 – 2020-10-15 21:49:42
A report by scFlow